calcGraphStats             package:ScISI             R Documentation

_A _f_u_n_c_t_i_o_n _t_o _c_a_l_c_u_l_a_t_e _t_h_e _v_a_r_i_o_u_s _s_u_m_m_a_r_y _s_t_a_t_i_s_t_i_c_s _f_o_r _Y_2_H
_i_n_d_u_c_e_d _g_r_a_p_h_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes a putative protein complex (given by comp) and
     a list of bait to prey associations, and from these two data-sets
     computes various summary statistics on the induced Y2H graph which
     include: edge proportion of sampled nodes (baits to prey);
     estimated population mean nodal degree; proportion of sampled
     baits with hits to baits with no hits; the average out degree of
     baits; the proteins (bait and prey) which are not isolated; the
     number of connected components to the y2h graph, etc.

_U_s_a_g_e:

     calcGraphStats(comp, bait2PreyL)

_A_r_g_u_m_e_n_t_s:

    comp: The 'comp' argument is a character vector containing the
          constituent proteins of some putative protein complex

bait2PreyL: A named list of lists. Each name represents a particular
          Y2H experiment; within each experimental entry, there is two
          more lists: 1. bpList and 2. expList. bpList is a named list
          of character vectors; each name corresponds to a bait protein
          of that particular experiment, and the enry is a chracater
          vecotor of the hit proteins found as prey. the expList is a
          named list concerning experimental data: ActD gives the
          activation domain; GW is a logical denoting if the prey list
          is genome wide; and numBaits details the number of baits used
          in the experiment.

_D_e_t_a_i_l_s:

     For the bait2PreyL; use the the intactInfo.rda data-set of the
     package y2hStat.

_V_a_l_u_e:

 complex: A character vector of the constituent members of the proteinn
          complex of interest

complexBait: A character vector of those protein members which were
          also tested as baits in the y2h experiments

 b2CompP: A character vector of all proteins which were tested as baits
          in the y2h experiments and also found a prey in the complex
          of interest

 notBait: A character vector of those protein members which were not
          tested as baits

avgDegOut: The average out-degree of the bait proteins of the complex
          of interest

notIsolated: A character vector of proteins that showed experimental
          binary affiliation for some other complex member

y2hGraph: An instance of the class graph; a graphNEL induceds Y2H graph
          on the protein complex

popMeanDegree: The population mean degree derived from the bait
          proteins

edgeProp: The estimated edge proportions derived between undirected Y2H
          edges

 degBait: A named list; each name corresponds to each member of the
          protein complex with the entry the number of proteins to
          which it is adjacent

_A_u_t_h_o_r(_s):

     T Chiang

